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The only trainers (in the main series) you do encounter with shiny Pokemon are in Trainer Tower from Fire Red and Leaf Green (Gen 3). In the Single Battle mode, the seventh Trainer has a shiny Meowth. In Double Battle mode, the first trainer pair will have a shiny Espeon. In the Knockout mode, the fourth trainer will have a shiny Seaking.

Several trainers in Pokemon Battle e (also Gen 3) have Pokémon that are shiny.

In B2/W2, you can encounter a shiny wild level 60 Haxorus in the middle of the Nature Preserve.